Design and validation of an STR hexaplex assay for DNA profiling of grapevine cultivars

Jiří Drábek; Michaela Smolíková; Ruslan Kalendar; Fernando A.Lopes Pinto; Pavel Pavloušek; Karel Klepárník; Ivo Frébort

doi:10.1002/elps.201600068

Design and validation of an STR hexaplex assay for DNA profiling of grapevine cultivars

Jiří Drábek, Michaela Smolíková, Ruslan Kalendar, Fernando A.Lopes Pinto, Pavel Pavloušek, Karel Klepárník, Ivo Frébort

Research output: Contribution to journal › Article › peer-review

4 Citations (Scopus)

Abstract

Although the analysis of length polymorphism at STR loci has become a method of choice for grape cultivar identification, the standardization of methods for this purpose lags behind that of methods for DNA profiling in human and animal forensic genetics. The aim of this study was thus to design and validate a grapevine STR protocol with a practically useful level of multiplexing. Using free bioinformatics tools, published primer sequences, and nucleotide databases, we constructed and optimized a primer set for the simultaneous analysis of six STR loci (VVIi51, scu08vv, scu05vv, VVMD17, VrZAG47, and VrZAG83) by multiplex PCR and CE with laser-induced fluorescence, and tested it on 90 grape cultivars. The new protocol requires subnanogram quantities of the DNA template and enables automated, high-throughput genetic analysis with reasonable discriminatory power. As such, it represents a step toward further standardization of grape DNA profiling.

Original language	English
Pages (from-to)	3059-3067
Number of pages	9
Journal	Electrophoresis
Volume	37
Issue number	23-24
DOIs	https://doi.org/10.1002/elps.201600068
Publication status	Published - Dec 1 2016
Externally published	Yes

Keywords

Grapevine DNA analysis
Multiplex PCR
STRs
Vitis vinifera L

ASJC Scopus subject areas

Analytical Chemistry
Biochemistry
Clinical Biochemistry

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1002/elps.201600068

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abstract = "Although the analysis of length polymorphism at STR loci has become a method of choice for grape cultivar identification, the standardization of methods for this purpose lags behind that of methods for DNA profiling in human and animal forensic genetics. The aim of this study was thus to design and validate a grapevine STR protocol with a practically useful level of multiplexing. Using free bioinformatics tools, published primer sequences, and nucleotide databases, we constructed and optimized a primer set for the simultaneous analysis of six STR loci (VVIi51, scu08vv, scu05vv, VVMD17, VrZAG47, and VrZAG83) by multiplex PCR and CE with laser-induced fluorescence, and tested it on 90 grape cultivars. The new protocol requires subnanogram quantities of the DNA template and enables automated, high-throughput genetic analysis with reasonable discriminatory power. As such, it represents a step toward further standardization of grape DNA profiling.",

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doi = "10.1002/elps.201600068",

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AU - Drábek, Jiří

AU - Smolíková, Michaela

AU - Kalendar, Ruslan

AU - Pinto, Fernando A.Lopes

AU - Pavloušek, Pavel

AU - Klepárník, Karel

AU - Frébort, Ivo

PY - 2016/12/1

Y1 - 2016/12/1

N2 - Although the analysis of length polymorphism at STR loci has become a method of choice for grape cultivar identification, the standardization of methods for this purpose lags behind that of methods for DNA profiling in human and animal forensic genetics. The aim of this study was thus to design and validate a grapevine STR protocol with a practically useful level of multiplexing. Using free bioinformatics tools, published primer sequences, and nucleotide databases, we constructed and optimized a primer set for the simultaneous analysis of six STR loci (VVIi51, scu08vv, scu05vv, VVMD17, VrZAG47, and VrZAG83) by multiplex PCR and CE with laser-induced fluorescence, and tested it on 90 grape cultivars. The new protocol requires subnanogram quantities of the DNA template and enables automated, high-throughput genetic analysis with reasonable discriminatory power. As such, it represents a step toward further standardization of grape DNA profiling.

AB - Although the analysis of length polymorphism at STR loci has become a method of choice for grape cultivar identification, the standardization of methods for this purpose lags behind that of methods for DNA profiling in human and animal forensic genetics. The aim of this study was thus to design and validate a grapevine STR protocol with a practically useful level of multiplexing. Using free bioinformatics tools, published primer sequences, and nucleotide databases, we constructed and optimized a primer set for the simultaneous analysis of six STR loci (VVIi51, scu08vv, scu05vv, VVMD17, VrZAG47, and VrZAG83) by multiplex PCR and CE with laser-induced fluorescence, and tested it on 90 grape cultivars. The new protocol requires subnanogram quantities of the DNA template and enables automated, high-throughput genetic analysis with reasonable discriminatory power. As such, it represents a step toward further standardization of grape DNA profiling.

KW - Grapevine DNA analysis

KW - Multiplex PCR

KW - STRs

KW - Vitis vinifera L

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Design and validation of an STR hexaplex assay for DNA profiling of grapevine cultivars

Abstract

Keywords

ASJC Scopus subject areas

UN SDGs

Access to Document

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